It remains difficult in theory and in practice to produce high-quality, highly contiguous genome sequences. High-throughput sequencing allows genetic analysis of the organisms that inhabit a wide variety of environments of biomedical, ecological, or biochemical interest. Shotgun sequencing of environmental samples, which often contain microbes that are refractory to culture, can reveal the genes and biochemical pathways present within the organisms in a given environment. Careful filtering and analysis of these data can also reveal signals of phylogenetic relatedness between reads in the data. However, high-quality de novo assembly of these highly complex datasets is generally considered to be intractable.